2dd8: Difference between revisions

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 ==Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody==
-<StructureSection load='2dd8' size='340' side='right' caption='[[2dd8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='2dd8' size='340' side='right'caption='[[2dd8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dd8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvhsa Cvhsa] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dd8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ajf|2ajf]], [[1za6|1za6]], [[2g75|2g75]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">recombinant antibody Fab ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Tor2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227859 CVHSA])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd8 OCA], [https://pdbe.org/2dd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd8 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd8 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd8 OCA], [http://pdbe.org/2dd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dd8 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SPIKE_CVHSA SPIKE_CVHSA]] S1 attaches the virion to the cell membrane by interacting with human ACE2 and CLEC4M/DC-SIGNR, initiating the infection. Binding to the receptor and internalization of the virus into the endosomes of the host cell probably induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.  S2 is a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.
+[https://www.uniprot.org/uniprot/Q8N355_HUMAN Q8N355_HUMAN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2dd8_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 30: / Line 29: @@
 </div>
 <div class="pdbe-citations 2dd8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Sandbox 3001|Sandbox 3001]]
+*[[Spike protein 3D structures|Spike protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cvhsa]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
+[[Category: Large Structures]]
-[[Category: Dimitrov, D S]]
+[[Category: Severe acute respiratory syndrome-related coronavirus]]
-[[Category: Feng, Y]]
+[[Category: Dimitrov DS]]
-[[Category: Gan, J H]]
+[[Category: Feng Y]]
-[[Category: Ji, X]]
+[[Category: Gan JH]]
-[[Category: Prabakaran, P]]
+[[Category: Ji X]]
-[[Category: Xiao, X D]]
+[[Category: Prabakaran P]]
-[[Category: Zhu, Z Y]]
+[[Category: Xiao XD]]
-[[Category: Antibody]]
+[[Category: Zhu ZY]]
-[[Category: Epitope]]
-[[Category: Immune system-viral protein complex]]
-[[Category: Inhibitor]]
-[[Category: S protein]]
-[[Category: Sar]]
-[[Category: Vaccine]]